Groovy Map containing riboseq sample information
e.g. `[ id:‘sample1’, single_end:false ]
bam_ribo
:file
Sorted riboseq BAM file(s)
*.{bam}
bai_ribo
:file
Index for sorted riboseq bam file(s)
*.{bai}
meta2
:map
Groovy Map containing TI-Seq sample information
e.g. [ id:'sample1', single_end:false ]
bam_ti
:file
Sorted TI-Seq BAM file(s)
*.{bam}
bai_ti
:file
Index for sorted TI-Seq BAM file(s)
*.{bai}
meta3
:map
Groovy Map containing reference information
e.g. [ id:'Ensembl human v.111' ]
fasta
:file
Fasta-format sequence file for reference sequences used in the bam file
*.gtf
gtf
:file
GTF-format annotation file for reference sequences used in the bam file
*.gtf
meta4
:map
Groovy Map containing information on candidate ORFs
candidate_orfs
:file
3-column (transIDstarttstop) candidate ORFs file
*.txt
meta5
:map
Groovy Map containing information on riboseq P-site offset parameter
files
para_ribo
:file
Input P-site offset parameter files for riboseq bam files
*.py
meta6
:map
Groovy Map containing information on TI-seq P-site offset parameter
files
para_ti
:file
Input P-site offset parameter files for TI-seq bam files
*.py
meta7
:map
Groovy Map containing reference information for the secondary
annotation file
reference_gtf
:file
Optional secondary GTF annotation passed to ribotish as
-a <reference-annotation> (e.g. a MANE/RefSeq overlay applied on
top of the primary GTF). Pass [] to omit.
*.gtf
Output
name:type
description
pattern
predictions
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*_pred.txt
:file
txt file all possible ORF results that fit the thresholds
*.{txt}
all
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*_all.txt
:file
txt file similar to the predictions but do not use FDR (q-value) cutoff
*.{txt}
transprofile
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*_transprofile.py
:file
Output RPF P-site profile for each transcript. The profile data is in
python dict format, recording non-zero read counts at different
positions on transcript.
